Merge pull request #74 from waterflow80/fix-for-issue-70

Checking for undefined attributes that could be sent by the user in the comparison POST request
EBIvariation · Jan 8, 2024 · 4d82114 · 4d82114
2 parents ca90fc9 + ca954c0
commit 4d82114
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Showing 3 changed files with 24 additions and 7 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColExtendedDataEntity.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColExtendedDataEntity.java
@@ -7,6 +7,7 @@
 import org.hibernate.annotations.TypeDefs;
 
 import uk.ac.ebi.eva.evaseqcol.digests.DigestCalculator;
+import uk.ac.ebi.eva.evaseqcol.exception.AttributeNotDefinedException;
 import uk.ac.ebi.eva.evaseqcol.model.NameLengthPairEntity;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONExtData;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONIntegerListExtData;
@@ -71,7 +72,7 @@ public static AttributeType fromAttributeVal(String attrVal) {
                     return b;
                 }
             }
-            throw new IllegalArgumentException("No seqcol attribute with value " + attrVal + " found");
+            throw new AttributeNotDefinedException("No seqcol attribute with value \"" + attrVal + "\" found");
         }
     }
 

diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/exception/AttributeNotDefinedException.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/exception/AttributeNotDefinedException.java
@@ -0,0 +1,11 @@
+package uk.ac.ebi.eva.evaseqcol.exception;
+
+/**
+ * This exception should be thrown when an undefined seqcol attribute has
+ * been given (normally by the user in the POST comparison request's body)*/
+public class AttributeNotDefinedException extends RuntimeException{
+
+    public AttributeNotDefinedException(String msg) {
+        super(msg);
+    }
+}
diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java
@@ -14,6 +14,7 @@
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColExtendedDataEntity;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelTwoEntity;
+import uk.ac.ebi.eva.evaseqcol.exception.AttributeNotDefinedException;
 import uk.ac.ebi.eva.evaseqcol.exception.DuplicateSeqColException;
 import uk.ac.ebi.eva.evaseqcol.exception.SeqColNotFoundException;
 import uk.ac.ebi.eva.evaseqcol.exception.UnableToLoadServiceInfoException;
@@ -377,12 +378,16 @@ public Map<String, String> constructSeqColLevelOneMap(Map<String, List<?>> seqCo
         Map<String, String> seqColL1Map = new TreeMap<>();
         Set<String> seqColAttributes = seqColL2Map.keySet(); // The set of the seqCol attributes ("lengths", "sequences", etc.)
         for (String attribute: seqColAttributes) {
-            String attributeDigest;
-            attributeDigest= digestCalculator.getSha512Digest(
-                    convertSeqColLevelTwoAttributeValuesToString(seqColL2Map.get(attribute),
-                                                                 SeqColExtendedDataEntity.AttributeType.fromAttributeVal(
-                                                                         attribute)));
-            seqColL1Map.put(attribute, attributeDigest);
+            try {
+                String attributeDigest;
+                attributeDigest= digestCalculator.getSha512Digest(
+                        convertSeqColLevelTwoAttributeValuesToString(seqColL2Map.get(attribute),
+                                                                     SeqColExtendedDataEntity.AttributeType.fromAttributeVal(
+                                                                             attribute)));
+                seqColL1Map.put(attribute, attributeDigest);
+            } catch (AttributeNotDefinedException e) {
+                logger.warn(e.getMessage());
+            }
         }
         return seqColL1Map;
     }